updates from paper analyses for HIV, TB and malaria #1147
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: "master" | |
| tags: ["*"] | |
| pull_request: | |
| paths: | |
| - .github/workflows/tests.yml | |
| - requirements/** | |
| - resources/** | |
| - src/tlo/** | |
| - tests/** | |
| - pyproject.toml | |
| - tox.ini | |
| schedule: | |
| - cron: 0 0 * * * | |
| # Force cancellation of in-progress workflows if changes are made to | |
| # the HEAD of the branch the workflow is currently running on. | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| # master branch will be allowed to have pending jobs | |
| # https://stackoverflow.com/a/70972844 | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/master' }} | |
| env: | |
| LD_PRELOAD: /lib/x86_64-linux-gnu/libSegFault.so | |
| SEGFAULT_SIGNALS: all | |
| jobs: | |
| gen-test-matrix: | |
| name: Find test files | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| # No tests should be under LFS so no need to fetch LFS files | |
| lfs: false | |
| - id: set-matrix | |
| name: Set matrix | |
| run: | | |
| set -e | |
| # Find all test files and generate their list in JSON format | |
| VAR_FILES="{\"include\":[" | |
| for file in tests/test_*.py; do | |
| VAR_FILES="${VAR_FILES}{\"file\":\"${file}\"}," | |
| done | |
| VAR_FILES="${VAR_FILES}]}" | |
| echo $VAR_FILES | |
| echo "matrix=${VAR_FILES}" >> $GITHUB_OUTPUT | |
| test: | |
| needs: gen-test-matrix | |
| name: Test ${{ matrix.file }} | |
| runs-on: [self-hosted, test] | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.gen-test-matrix.outputs.matrix) }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: System info | |
| run: | | |
| set -x | |
| python3 --version | |
| uname -a | |
| lsb_release -a | |
| virtualenv --version | |
| pip --version | |
| tox --version | |
| - name: Test with tox | |
| run: | | |
| tox -v -e py311,report -- pytest --cov --cov-report=term-missing -vv "${{ matrix.file }}" |